OEChem TK 2.1.3¶
The InChI code has been updated to the v1.05 source released on January 27, 2017. This code is available from the InChI Trust and was validated against eMolecules and ChEMBL_23 public structure sources.
InChI is now a fully supported read/write format for chemical structures. New public API points have been added to support this format:
The standard InChI format includes chemical normalization activity that
results in round-trip structure alterations to a very high percentage of
structures when unnormalized or when arbitrary input chemistry is used.
Even the output of
OEMolToInChI, which generates a
nonstandard InChI and attempts to minimize structure normalizations, results
in many changes to input chemical structures.
The default output flavor for writing InChI or InChIKey via
OEWriteMoleculehas been changed to include the molecule title as well as the InChI information to synchronize behavior with other output formats. Since the InChI identifiers never include white space, there should be no ambiguity for separating the InChI information from the title. If there are third-party readers that have problems with the title, the following output flavor bits are now available to control whether the title is added to the output:
An overload of
OEShortestPathhas been added to take an atom predicate and return the shortest path between atoms that are not excluded by the predicate.
Minor bug fixes¶
OEGetSmiStringOrdernow has both a
OEGetSmiStringOrdercould crash for structures that were modified by deleting atoms. This has been fixed.
OESystem TK 2.1.3¶
A new parameter has been added to the constructor of OEDots that enables changing the “processed” label in the output lines.
OEBio TK 2.1.3¶
OESetupSplitMolComplexOptionsnow has two additional parameters,
modelOverride, that make it easier to configure filters while iterating over binding sites and/or model numbers. The new constant
OESplitMolComplexParam_DoNotOverrideis used control the behavior of these constants.
A new atom predicate, OEIsWater, has been added.
Two new interaction hint types have been added to interaction perceptions: OECovalentInteractionHint and OECationPiInteractionHint. When covalent interactions are present, nearby clash interactions are no longer perceived.
The OECrystalSymmetryParams class now stores the Z-value parsed from the
CRYST1line of a PDB file.
Minor bug fixes¶
GetGroupsno longer crashes on Windows in cases where no alternate location group exists.
Calling the function
OEBuildUnitCellon protein molecules had previously consumed large amounts of memory and, as a result, would often crash. This issue has been addressed, and the performance of the function has been improved for molecules of small or medium size.
Interaction perception for anionic carbonyl groups has been fixed.
OEIsValidActiveSitenow takes into account the non-default parameter ligand component type.
OEGrid TK 1.6.0¶
Minor bug fixes¶
OEMaskGridByMoleculeno longer segfaults for an empty molecule or for a molecule without 2D coordinates. It now throws a warning and returns
On Windows, UTF8 file and directory names are now correctly supported for toolkit file I/O operations.
Read/write examples have been added to demonstrate the use of the InChI structure format.